I thought that you needed to reflash the computer to get it up and running. I'll be running stock for a while as its a big power improvement on what I currently have.
I rewired my harness and got mine running on the stock computer. I'm not far enough along to take it on the road yet to see if there are any trans or other issues though. If it has the SKIM (security) I think you have to have it reflashed. I am still undecided on if I should get a predator with a custom tune to disable the rear O2 sensors so I don't have to run cats. If I do that I will likely get a different cam as well to make it more worthwhile.